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Saturday, December 4, 2010

Arsenic and Old News?

"Arsenite...[incorporates into DNA] in the place of phosphate in the nucleotides during the synthesis of DNA."

You've seen this story all over the web in the last few days. Alien life! Life on other planets!! NASA is revived! Mars men get ready, 'cause here we come!

But, in fact, is that really the story?

The report was published in Science Express this week andwritten about in the NYT -- and everywhere else you look:

Scientists said Thursday that they had trained a bacterium to eat and grow on a diet of arsenic, in place of phosphorus — one of six elements considered essential for life — opening up the possibility that organisms could exist elsewhere in the universe or even here on Earthusing biochemical powers we have not yet dared to dream about.

“There is basic mystery, when you look at life,” said Dimitar Sasselov, an astronomer at the Harvard-Smithsonian Center for Astrophysics and director of an institute on the origins of life there, who was not involved in the work. “Nature only uses a restrictive set of molecules and chemical reactions out of many thousands available. This is our first glimmer that maybe there are other options.”

NASA, naturally enough, with its PR army always at the ready to instantly toot its own horn, didn't miss this juicy chance:

NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

So some bacteria were artificially selected to eat arsenic. What's the big deal here? Is this a big deal?

Caleb Scharf, an astrobiologist at Columbia University who was not part of the research, said he was amazed. “It’s like if you or I morphed into fully functioning cyborgs after being thrown into a room of electronic scrap with nothing to eat,” he said.

Oh, that's it! It is a big deal! The bacteria morphed into cyborgs! Or rather, the arsenic insinuated itself into the bacterial DNA, by replacing phosphates in some of the nucleic acids. Is that a big deal?

That quote we started with?
It turns out that that quote with which we lead this post, in red, the one about arsenite incorporating into DNA, the big finding that NASA is touting, is from a paper published in 1980 -- 30 years ago -- about the health effects of arsenic and how and why it's so toxic. To humans. Give humans enough arsenic and they die, but we can survive lower levels. Kind of like bacteria. And that 1980 paper cites a 1974 paper, Petres, J., D. Baron and I. Kunick, Untersuchungen fiber arscnbedingte VerKndenmgen der Nueleinsauresynthase in vitro, Derm. Mschr., 160 (1974) 724--729 -- ok, it's in German, but it's still knowledge that's out there.)

Something largely new, worth knowing--important, even!
It's long been known that Arsenic is chemically similar to Phosphorous and can substitute in many biomolecueles, like protein and DNA, and their reactions. This is freshman chemistry. It has also been known that the arsenic alternatives are less stable than those involving phosphorous in these compounds and reactions.

What this new study showed was that these particular bacteria, chosen because they had already adapted to a high-aresenic environment, could be induced by artificial selection pressure to incorporate arsenic into their basic biomolecules. The study is a careful, sophisticated demonstration of this fact. The authors clearly state that the bacteria were already adapted--in the normal evolutionary way--to high-aresenic environment. What they then did was gradually feed a serially transferred culture of these bugs to increasing concentrations of arsenic and little or no added phosphorous. The bacteria that survived were able to substitute the arsenic for some, at least, of their biofunctions (including use to synthesize DNA).

This is worthy of publication in a major journal, and even newsworthy as showing the degree to which already adapted simple organisms can adapt further to a slowly changed environment. It shows the potential power of evolutionary adaptation, and the degree to which life could, in some ways, function in an arsenic, phosphorous-deprived environment.

But this is not a new life form, any more than a giraffe is a new life form. The idea that there is life that doesn't function exactly as we do is not new. After all, we have found anaerobic life, life in extremely hot, cold, salty etc. conditions on Earth. In most every way, these are ordinary bacteria and this is ordinary evolution followed by very carefully imposed artificial selection.

Were they happy?
And those little bacteria? They were much much happier when given phosphorus again after their arsenic bath. As the authors say, the bacterium "is not an obligate arsenophile and it grew considerably better when provided with P" [phosphorus] -- which means that it would not have survived natural selection in the presence of both chemicals.

Indeed, this study doesn't provide a scrap of evidence that such forms could evolve into stable complex life forms de novo without the help of strong, intentional, teleological and hence totally non-Darwinian evolution. Maybe it's possible, but this study shows nothing more than that bioreactions can occur, under some particular conditions, with the incorporation of arsenite in a complex cell already adapted to an arsenic environment. We aren't chemists so can't say how much this study furthers, if not really revolutionizes, ordinary biochemistry. The paper basically says nothing about life in NASA-land. That was almost entirely PR hyperbole--the usual self-promotion (not, we note, by the authors in their paper, though they were funded by NASA).

This paper can stand on its own legs as an interesting finding in biochemistry, or even a demonstration of the power of natural or artificial selection....but is there anything new here that wasn't already known in the 1974 German paper? Perhaps the latter (we don't read German well enough to judge) was an in vitro reaction rather than one occurring in a whole organism. If so, if this is a new finding about DNA synthesis in vivo, then responsible news media should just say that without all the ballyhooing and showmanship.

Do we know anything new about alien life?
As to alien life, what does this add? Let's now assume that the study shows that, in principle, life could exist without phosphorous and with arsenic. It has long been argued (wholly hypothetically, but let's not quibble about that either) that if there are billions of rocky planets in the universe (and, perhaps it's trillions, and perhaps there are many universes) and if even only a tiny fraction of those planets have classical earth-life conditions, then just statistically there must be thousands of planets with life that has at least some similarities with our own. That doesn't mean they use DNA with RNA intermediates, have brains or lipid cell membranes (or cells, for that matter). But even assuming that is statistically possible, it may exist on at least some planets somewhere out there. The larger space is, the more of these there statistically would be, on the basis just of probability. Of course such numbers games are fun, but prove nothing.

So what about the arsenic finding? Suppose, say, it doubled the fraction of planets that would have this additional life-possible make-up. By playing the same numbers game, this would just raise the hypothetical number of planets with life on them by, say, a factor of two. It doesn't change a single thing we've thought or known before. Even if we assumed that the new result showed that arsenic could work.

It also doesn't raise by any serious amount the likelihood we'll find such planets, that we'll talk to the little green arseno-Men who live on them, or anything else.

Are we condemned to live in a world in which everything has to be boasted about, or turned into entertainment? Is it OK for science to be turned into fun in this way? Or is it irresponsible?

Science is interesting in its own right, and we know that, left alone, it will lead, if unpredictably, to increased and interesting knowledge, and improved standards of living. But the hype-route obviously isn't working to make a population that's more deeply understanding of science. It makes a population that (in the US) largely doesn't even 'believe' in evolution, and perhaps increasingly can't tell fact from fiction.

8 comments:

This finding redresses the undue attention origin-of-life researchers have paid to life's particular molecular composition. It implies that what makes biological life 'special' isn't necessarily what constructs it but how it's constructed.

Though the periodic table provides a start, we can begin to treat life's chemistry as a set of constraints contingent to where an organism developed.

As life belongs to a more general class of phenomena far from thermodynamic equilibrium, it would make sense to focus on the general structures that can arise in such states and in the process expand our definition of life.

In the above example we see that contingent chemistry is in fact a medium for such structures.

Therefore, looking for water on other astronomical bodies doesn't necessarily present itself as the best means by which to gauge the plausibility of life inhabiting said bodies.

I wouldn't disagree with any of this. We generally have a problem if we have to specify 'life' as in the image and likeness of earth, so to speak. I think we said nothing contrary to your perspective.

I think you hit the nail on the head with the phrase 'contingent chemistry'. But what people (certainly the public, and I think privately most scientists) really dream about is life-as-we-know-it: 'bacteria' or complex organisms with 'intelligence' of a sort we'd recognize (that is, we don't recognize flies as being 'intelligent' in the SETI sense!).

Also, even prominent scientists have argued that upright, limbed, bilateral symmetric organisms with cognitive abilities that we'd recognize, are nearly inevitable somewhere in the cosmos.

And of course people want to predict that 'life' has to be like ours (carbon, water, etc. etc.) because it is natural to hunger for companionship in the universe. Otherwise, who cares if it's silicon based or whatever?

Bluntly speaking, NASA needs something Hollywood would like because that's the only way they will pry huge budgets out of the public--because then they can find planets (like Mars) that they can say we absolutely must go to (urgently!).

Likewise, 'life' has to be something other than, say, self-replicating proliferation of slimy blogs or crystals. It has to be something that one can make movies about, or talk to. Otherwise, funding won't be there.

That, in a sense, is why NASA provides a lot of funding for 'astrobiology' and in that sense why this arsenic study could be funded by them. But whether NASA's budget for that kind of research should be cut, and the funds given to NSF where the objectives of understanding early earth life (which is what most of the funded researchers do) would be perfectly legitimate, is a separate question.

And, Arjun, one more thing: this research says nothing that is so terribly new or that has any convincing basis for arguments about extra-terrestrial life. We didn't raise some important questions about that, but we did note that arsenic is not a stable substitute for phosphorous. So, for example, a planet with both arsenic and phosphorous would evolve life around the latter, not the former, and would not thus raise the odds of life (on such planets) by any useful amount.

In my above comment I aimed to emphasize that in considering life and its origins we have instituted multiple paradigms of thought (some of which remain unconscious), one of which was the implausibility of organisms built with anything but a small set of elements.

NASA opens their public announcement with:

"NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth."

I maintain that new and enlightening avenues of research lie dormant and will continue to do so until we relax certain assumptions about what life can be. What NASA refers to as "fundamental knowledge" in fact represents such a paradigm.

For another example, what seems to be a fervent belief in life evolving only in certain directions prevents many from considering the virus a form of life (unless of course the virus preceded cellular life). One assumption in place here is that the cell is the basic unit of life, but is such a requirement arbitrary? What about the other rules which 'define' life? At best they all appear to be characteristics common to all of that which we have ordained to be life on Earth prior to the discovery of such structures as viruses.

You make some more good and relevant points. Even taking the Strong Poison paper on its own terms, before one makes any conclusions, the authors should show that all of DNA (for example, no matter what the adjacent nucleotides are) and all basic biochemical reactions, can occur with arsenic and no phosphorous present.

Short of that, the current paper only shows that arsenic can substitute for at least some functions of phosphorous in its major classes (proteins, interactions, DNA,...).

If it's already less than very stable, and if it can't undertake all of what would be needed in life as we know it, then even NASA's dreamworld extrapolation of the work to planets-they-want-money-to-investigate is even more thinly justified at best.

"I was outraged at how bad the science was," University of British Columbia microbiology professor Rosie Redfield.

"This paper should not have been published," University of Colorado molecular biology professor Shelley Copley.

"I suspect that NASA may be so desperate for a positive story that they didn't look for any serious advice from DNA or even microbiology people," UC-Davis biology professor John Roth told Zimmer.

A NASA spokesperson brushed off the criticism. The paper's authors have not responded to the firestorm. Needless to say, that posture, too, has drawn the ire of critics. "That's kind of sleazy given how they cooperated with all the media hype before the paper was published," Redfield said.

We are in an era of shameless self-promotion. As far as integrity goes, a substantial fraction of our citizens make their living misrepresenting various vested interests. It's our way manoevering for resources, and maybe it's not worse than other political systems. But it's sad, to me anyway.

NASA seems absolutely shameless in this regard, but are they worse than, say, NIH in this? We expect it from companies like detergent, car, or cereal companies, but not from non-commercial organizations.

NASA has a budget (substantial, I think) for 'astrobiology', which sounds sexy and cool but of those investigators I know supported by them the research has nothing to do with 'astro' biology, but with the origins of earth life.

Nothing wrong with that, as we said in our post on the arsenic story. But it should be funded by NSF and justified on its own terms, rather than being largely, at least, a PR activity of NASA's. For genuine questions about extraterrestrial life, or things related to that, then of course NASA might be a natural supporter of it. But that is not really how things are working at present (and the NASA-supported investigators know it).

Again, the research itself is interesting (unless experts find flaws that I'm not qualified to find). But not the hype.

NASA's spin doctors' clinic is open for business again today. The news story mentions various things in the context of extraterrestrial life, including arsenic-men, but I add this comment today because they invoke the statistical likelihood kind of argument.

They cite recent data suggesting something on the order of sextillion planets that may exist, and that new telescopic methods may be able to detect many specific ones.

So far so good, but of course they have to turn an interesting advance in astronomy by linking it to Hollywood---what this says about life out there in the Vast Beyond.

Of course as we noted in our arsenic post, this actually says essentially nothing about that that we didn't already know: if life is possible (and we seem to be proof that it is!) and if it's just chemicals reacting (and scientific laws assume uniformity everywhere), then the plausibility or likelihood of life out there is just a matter of statistical probability.

We have zero real idea about what that probability is, or even if 'probability' is an appropriate word to describe what we think about life There. What the word would mean is that some fraction, p, of planets have life (or, depending on how Hollywood you want to be, smart earth-like life made of beings we'd like to invite to dinner). The value p in this sense would reflect the chance that a random planet you happened to land the Enterprise on would have little arsenic men onit.

Can we assert that the probability is, say, 0.00001 per planet? Or is it 0.0000001? Or is it 0.000000027564832?

Really, all we can say is that p>0.0. And that is a statement based entirely on the assumptions stated above.

Nothing wrong with that, except that NASA's 'science' spinners want you to believe it's much more soundly based....and hence, let's give NASA lots of funding to go out there with a big butterfly net to grab 'em and bring 'em back to earth.

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